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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catctcttgtggtgttcagtttgttgctttcatgggcatgtgtgggatgtgcgacttggagggtaagcaaagtgtgactgggtggatgtgagtattgtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTTCTACAGTACTCTCCAAATCTGCGATGCAATGCT

Basic information

species Physcomitrella patens
transcript PP1S60_100V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 10
catctcttgtggtgttcagtttgttgctttcatgggcatgtgtgggatgtgcgacttggagggtaagcaaagtgtgactgggtggatgtgagtattgt-agGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTTCTACAGTACTCTCCAAATCTGCGATGCAATGCT
             || |      |     | |   |||| | | |  |||    ||       | |  ||| | | | |   |  || |   | |||  || ||||||||||||||||||| |||||||| || ||  ||||||||||||| || ||||||||||| ||||| || ||||  |||
-------------gtactagaaatcaaagtaa-atgcatatatagtttgtttctctcatcttatca-taaatttttatttattc-atatccttgttgccagATATTCCATAAACGCATGCCTCCAGAAGCTGTTGATTTGGTTTCAAGACTACTGCAGTACTCTCCTAATCTACGGTGCACAGCT

upper sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv14s0066g01050.t01 (Vitis vinifera), 3'ss of exon 10
catctcttgtggtgttcagtttgttgctttcatgggcatgtgtgggatgtgcgactt-ggagggtaagcaaagtgtgactgggtggatgtgagtatt-gtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTTCTACAGTACTCTCCAAATCTGCGATGCAATGCT
           |||  |  ||  || || |   |  ||| |     ||    |  || |||   |      | | |  |||      |     | || | || | || || || |||||||| ||||||||||| || || || || |||||||| || ||||||||||||||  | || | ||||
-----------gtgagctcttgatttctataccgaccatttcaataattgatgcttttggattttgtatcgaatttatctgaaaatgttctcttgtttgcagATTTTTCACAAGCGCATGCCCCCAGAAGCAGTAGATCTTGTCTCTAGACTTCTTCAATACTCTCCAAATCTAAGGTGTACTGCT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|37852721|gb|BJ610729.1|BJ610729
EST:     CTACACGGAGTTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA                         GTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
genomic: CTACACGGAG-TTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtc ... agtattgtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
EST: gi|162249128|gb|FC420379.1|FC420379
EST:     ACTACACGGAGTTCAAGTTTCCGCANATCAAGGCTCACCCATGGCACAAA                         GTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
genomic: ACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtc ... agtattgtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
EST: gi|37836905|gb|BJ594913.1|BJ594913
EST:     ACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA                         GTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
genomic: ACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtc ... agtattgtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
EST: gi|162249101|gb|FC420378.1|FC420378
EST:     ACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA                         GTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
genomic: ACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtc ... agtattgtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
EST: gi|18339293|gb|BJ171320.1|BJ171320
EST:     ACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA                         GTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
genomic: ACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtc ... agtattgtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
EST: gi|18333045|gb|BJ165059.1|BJ165059
EST:     TTCCGCAAATCAAGGCTCACCCATGGCACAAA                         GTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
genomic: TTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtc ... agtattgtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
EST: gi|162165970|gb|FC341801.1|FC341801
EST:     ACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA                         GTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
genomic: ACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtc ... agtattgtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
EST: gi|37837915|gb|BJ595923.1|BJ595923
EST:     AGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA                         GTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT
genomic: AGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtc ... agtattgtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 34 (downstream exon)
Score: 17

GTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtc ... agtattgtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTTCTACAGTACTCTCCAAATCTGCGATGCAATGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtgcgacttggagggtaagcaaagtgtgactgggtggatgtgagtattgtagGTATTCCATAAACGCATGCCACCAGAAGCAGTCGACCTGGTTTCAAGACTTCTACAGTACTCTCCAAATCTGCGATGCAATGCT
                                               tattgta  TA-rich tract